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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #322391
Title: Increasing the number of single nucleotide polymorphisms used in genomic evaluation of dairy cattle

Author
item Wiggans, George
item Cooper, Tabatha
item Vanraden, Paul
item Van Tassell, Curtis - Curt
item Bickhart, Derek
item SONSTEGARD, TAD - Former ARS Employee

Submitted to: Journal of Dairy Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/14/2016
Publication Date: 6/1/2016
Citation: Wiggans, G.R., Cooper, T.A., Van Raden, P.M., Van Tassell, C.P., Bickhart, D.M., Sonstegard, T.S. 2016. Increasing the number of single nucleotide polymorphisms used in genomic evaluation of dairy cattle. Journal of Dairy Science. 99(6):4504-4511.

Interpretive Summary: Since genomic evaluation of dairy cattle began in the United States in April 2008, a progression of genotyping chips has been employed, and genotypes from 18 chips had been submitted to the Council on Dairy Cattle Breeding for use in national genomic evaluations by the end of August 2015. One factor that drives the creation of new chips is that the pool of bead types used to manufacture a chip becomes exhausted, which provides an opportunity to update the SNP set when creating a new pool. GeneSeek designed a new version of its chip with 77,000 single nucleotide polymorphisms (SNPs). For the new chip, a set of over 140,000 SNPs was selected: all SNPs on the 77,000-SNP chip, all SNPs used in U.S. national genomic evaluations, SNPs that were possible functional mutations, and other SNPs with a low minor allele frequency to better track causative variants. A set of 77,321 SNPs was evaluated using August 2011 data to predict April 2015 performance to determine which SNPs should be included in genomic evaluations. The increase in evaluation accuracy over using the 60,671 SNPs currently used for genomic evaluation was 1.4 percentage points across traits for Holsteins. Revision of the set of SNP included in genomic evaluation is expected to be an ongoing process to increase evaluation accuracy by substituting more informative SNPs for less informative ones, particularly adding causative variants as they are discovered.

Technical Abstract: GeneSeek designed a new version of the GeneSeek Genomic Profiler HD BeadChip for Dairy Cattle, which had >77,000 single nucleotide polymorphisms (SNPs). A set of >140,000 SNPs was selected that included all SNPs on the existing GeneSeek chip, all SNPs used in U.S. national genomic evaluations, SNPs that were possible functional mutations, and other informative SNPs. Because SNPs with a lower minor allele frequency might track causative variants better, 30,000 more SNPs were selected from the Illumina Bovine HD Genotyping BeadChip by choosing SNPs to maximize differences in minor allele frequency between a SNP being considered and the 2 SNPs that flanked it. Single-gene tests were included if their location was known and bioinformatics indicated relevance for dairy cattle. To determine which SNPs from the new chip should be included in genomic evaluations, genotypes available from chips already in use were used to impute and evaluate the SNP set. Effects for 134,511 usable SNPs were estimated for all breed-trait combinations; SNPs with the largest absolute values for effects were selected (5,000 for Holsteins, 1,000 for Jerseys, and 500 each for Brown Swiss and Ayrshires for each trait). To increase overlap with the 60,671 SNPs currently used for genomic evaluation, 12,094 more SNPs with the largest effects were added. After removing SNPs with many parent-progeny conflicts, 84,937 SNPs remained. Three cutoff studies were conducted with 3 SNP sets to determine reliability gain over that for parent average when evaluations based on August 2011 data were used to predict December 2014 performance. Across all traits, mean Holstein reliability gains were 32.5, 33.4, and 32.0 percentage points for 60,671, 84,937, and 134,511 SNPs, respectively. After genotypes from the new chip became available, the proposed set was reduced from 84,937 to 77,321 SNPs to remove SNPs that were not included in production, reduce computing time, and improve imputation performance. The set of 77,321 SNPs was evaluated using August 2011 data to predict April 2015 performance. Reliability gain over 60,671 SNPs was 1.4 percentage points across traits for Holsteins. Improvement over 84,937 SNPs was partially the result of 4 months of additional data and genotypes from the new chip. Revision of the SNP set used for genomic evaluation is expected to be an ongoing process to increase evaluation accuracy.